I think everyone has their own system. As far as Base cards for sets go I Keep them In Numerical order of Sets. I then place them in 800 count boxes, and use the thick white cardboard fillers to seperate sets within one box, when it is nearly full I mark on the end of the 800 card box what sets are held within the box, Then I keep the boxes stacked up alphabetically by year. Took me a long time to get everything set up that way, but Now when I am looking for cards to fill someones set needs, it is very quick to see if I have anything for them.
All of my Inserts / #"ed/ GU /AU/ Parallels I keep in seperate boxes and type up a database for them.
That way with the database I can set filters to search out specific types of cards: If Someone is looking for Topps Inserts only I can open my Inserts Database, Set a filter to search for "sets containing Topps" and it will list everything I have in the Database that contains Topps in teh set name.
-Nick